It's worth noting that in some cases, Mega Drive ports of Amiga games were made with 50Hz in mind, and even in the cases where that wasn't so, I've found that the PAL-optimised versions were done well. If I'm remembering rightly, the Mega Drive version of Shadow of the Beast at 60Hz is impossibly hard, which earned it a panning in some countries, as it was a rare case of not optimising for NTSC markets. I'm pretty sure I'm remembering the right game, here - there was even a later Japan-only release meant to rectify it, if I recall correctly.
I think sometimes the ports are better than the originals, personally. The Legend of Galahad plays better than Leander in my book, thanks to the extra buttons, having both sound effects and music at the same time (it's nice to be able to hear what's going on!), and (admittedly far less importantly, but it adds polish and atmosphere) some graphical upgrades. Some or all of these also go for the likes of Wiz 'n' Liz, Puggsy, and Zool. (I'd say it applies to Another World, as well, but I personally feel that the SNES version of that is better than the Mega Drive one.)
Some ports are entirely different - in the Mega Drive version of Lemmings, for example, the vast majority of its 180 or so levels are unique to it, with very few being from the Amiga original (and even fewer being slightly altered versions of levels from Oh No! More Lemmings). It's worth picking up if you want to play more Lemmings levels. (I believe this also applied to the unreleased port of Bill's Tomato Game, as well, from what little I've seen about it.)
If we're to include the Mega CD as well, then the definitive version of The Misadventures of Flink (which I think was backported to the CD32, rather than vice-versa) is there, with a higher level of polish, as well as an upgraded version of Puggsy that has some extra stuff and added bosses. I'm told that the Mega CD version of Another World is very good, too, though I've not tried it myself.
I'd say it's worthwhile, personally (indeed, the Mega Drive versions are my preferred versions of some of these games), but it might be worth having a 50Hz/60Hz switch so that you can get the best of both worlds.